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Conserved domains on  [gi|2247866118|gb|URP22639|]
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RNA polymerase II largest subunit, partial [Gyroporus austrobrasiliensis]

Protein Classification

Graphical summary

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List of domain hits

 Name Accession Description Interval E-value
RNA_pol_Rpb1_1 super family cl29786
RNA polymerase Rpb1, domain 1; RNA polymerases catalyze the DNA dependent polymerization of ...
 8-110 1.53e-09

RNA polymerase Rpb1, domain 1; RNA polymerases catalyze the DNA dependent polymerization of RNA. Prokaryotes contain a single RNA polymerase compared to three in eukaryotes (not including mitochondrial. and chloroplast polymerases). This domain, domain 1, represents the clamp domain, which a mobile domain involved in positioning the DNA, maintenance of the transcription bubble and positioning of the nascent RNA strand.


The actual alignment was detected with superfamily member pfam04997:

Pssm-ID: 398595  Cd Length: 320  Bit Score: 53.45  E-value: 1.53e-09
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2247866118   8 KVRHVRDRKARMAIIWNHCKSKMNCETDEPREdgaegepeepkkghGGCGHQQPVIRKEGLKLFVQYKRPKDDdedmksm 87
Cdd:pfam04997 118 KRLGLENLKMGAKAILELCKKKDLCEHCGGKN--------------GVCGSQQPVSRKEGLKLKAAIKKSKEE------- 176

                          90       100
                  ....*....|....*....|...
gi 2247866118  88 qPDKRLFTPSEVYTTFKKMSDSD 110
Cdd:pfam04997 177 -EEKEILNPEKVLKIFKRISDED 198
 
Name Accession Description Interval E-value
RNA_pol_Rpb1_1 pfam04997
RNA polymerase Rpb1, domain 1; RNA polymerases catalyze the DNA dependent polymerization of ...
 8-110 1.53e-09

RNA polymerase Rpb1, domain 1; RNA polymerases catalyze the DNA dependent polymerization of RNA. Prokaryotes contain a single RNA polymerase compared to three in eukaryotes (not including mitochondrial. and chloroplast polymerases). This domain, domain 1, represents the clamp domain, which a mobile domain involved in positioning the DNA, maintenance of the transcription bubble and positioning of the nascent RNA strand.


Pssm-ID: 398595  Cd Length: 320  Bit Score: 53.45  E-value: 1.53e-09
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2247866118   8 KVRHVRDRKARMAIIWNHCKSKMNCETDEPREdgaegepeepkkghGGCGHQQPVIRKEGLKLFVQYKRPKDDdedmksm 87
Cdd:pfam04997 118 KRLGLENLKMGAKAILELCKKKDLCEHCGGKN--------------GVCGSQQPVSRKEGLKLKAAIKKSKEE------- 176

                          90       100
                  ....*....|....*....|...
gi 2247866118  88 qPDKRLFTPSEVYTTFKKMSDSD 110
Cdd:pfam04997 177 -EEKEILNPEKVLKIFKRISDED 198
 
Name Accession Description Interval E-value
RNA_pol_Rpb1_1 pfam04997
RNA polymerase Rpb1, domain 1; RNA polymerases catalyze the DNA dependent polymerization of ...
 8-110 1.53e-09

RNA polymerase Rpb1, domain 1; RNA polymerases catalyze the DNA dependent polymerization of RNA. Prokaryotes contain a single RNA polymerase compared to three in eukaryotes (not including mitochondrial. and chloroplast polymerases). This domain, domain 1, represents the clamp domain, which a mobile domain involved in positioning the DNA, maintenance of the transcription bubble and positioning of the nascent RNA strand.


Pssm-ID: 398595  Cd Length: 320  Bit Score: 53.45  E-value: 1.53e-09
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2247866118   8 KVRHVRDRKARMAIIWNHCKSKMNCETDEPREdgaegepeepkkghGGCGHQQPVIRKEGLKLFVQYKRPKDDdedmksm 87
Cdd:pfam04997 118 KRLGLENLKMGAKAILELCKKKDLCEHCGGKN--------------GVCGSQQPVSRKEGLKLKAAIKKSKEE------- 176

                          90       100
                  ....*....|....*....|...
gi 2247866118  88 qPDKRLFTPSEVYTTFKKMSDSD 110
Cdd:pfam04997 177 -EEKEILNPEKVLKIFKRISDED 198
 
Blast search parameters
Data Source: Precalculated data, version = cdd.v.3.21
Preset Options:Database: CDSEARCH/cdd   Low complexity filter: no  Composition Based Adjustment: yes   E-value threshold: 0.01

References:

  • Wang J et al. (2023), "The conserved domain database in 2023", Nucleic Acids Res.51(D)384-8.
  • Lu S et al. (2020), "The conserved domain database in 2020", Nucleic Acids Res.48(D)265-8.
  • Marchler-Bauer A et al. (2017), "CDD/SPARCLE: functional classification of proteins via subfamily domain architectures.", Nucleic Acids Res.45(D)200-3.
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